In 1989, in the George H. W. Bush administration, Zelikow was detailed to the National Security Council, where he was involved as a senior White House staffer in the diplomacy surrounding the German reunification and the diplomatic settlements accompanying the end of the Cold War in Europe.

During the first Gulf War, he aided President Bush, National Security Advisor Brent Scowcroft, and Secretary of State James Baker in diplomatic affairs related to the coalition.

[citation needed] In 1998, Zelikow moved to the University of Virginia, where until February 2005 he directed the nation's largest center on the American presidency.

[3] In a presidential oral history project headed by James Sterling Young, it systematically gathers additional information on the presidencies of Reagan, George H. W. Bush, and Clinton.

The United States might respond with draconian measures scaling back civil liberties, allowing wider surveillance of citizens, detention of suspects, and the use of deadly force.

After George W. Bush took office, Zelikow was named to a position on the President's Foreign Intelligence Advisory Board [PFIAB], and worked on other task forces and commissions as well.

The Task Force comprises a diverse and bipartisan group of experienced policymakers, senior executives from the information technology industry, public interest advocates, and experts in privacy, intelligence, and national security.

[14] In Rise of the Vulcans (2004), James Mann reports that when Richard Haass, a senior aide to Secretary of State Colin Powell and the director of policy planning at the State Department, drafted an overview of America's national security strategy following the September 11, 2001 attacks, Dr. Rice, the national security advisor, "ordered that the document be completely rewritten.

[17] In 2014–15, while on leave from the University of Virginia and working for the Markle Foundation, Zelikow helped lead a Foundation-sponsored group of prominent Americans called "Rework America."

He is named by sources such as Jack Goldsmith's The Terror Presidency as an internal critic of the treatment of terrorist captives, and there was wide attention given to an address he made on this subject after leaving office in April 2007.

[citation needed] Based on speeches and internal memos, some political analysts believe that Zelikow disagreed with aspects of the Bush administration's Middle Eastern policy.

[22][23] Jane Mayer, author of The Dark Side,[24] quotes Zelikow as predicting that "America's descent into torture will in time be viewed like the Japanese internments", in that "(f)ear and anxiety were exploited by zealots and fools.

They observed, as Zelikow noted in his own words, that "contemporary" history is "defined functionally by those critical people and events that go into forming the public's presumptions about its immediate past.

"[27] Zelikow has also written about terrorism and national security, including a set of Harvard case studies on "Policing Northern Ireland."

In the November–December 1998 issue of Foreign Affairs, he co-authored an article Catastrophic Terrorism, with Ashton B. Carter, and John M. Deutch, in which they speculated that if the 1993 bombing of the World Trade Center had succeeded, "the resulting horror and chaos would have exceeded our ability to describe it.

It could involve loss of life and property unprecedented in peacetime and undermine America’s fundamental sense of security, as did the Soviet atomic bomb test in 1949.

The United States might respond with draconian measures scaling back civil liberties, allowing wider surveillance of citizens, detention of suspects and use of deadly force.

Zelikow emphasizes that German Chancellor Bethmann Hollweg was seriously interested in peace, but he had to fend off the demands of Paul von Hindenburg and Erich Ludendorff who were taking dictatorial control of Germany.